Genome-wide analysis of hepatic gene silencing in mammalian cell hybrids.

Abstract:

:Silencing of tissue-specific gene expression in mammalian somatic cell hybrids is a well-documented epigenetic phenomenon which is both profound (involving a large number of genes) and enigmatic. Our aim was to utilize whole-genome microarray analyses to determine the true extent of gene silencing on a genomic level. By comparing gene expression profiles of hepatoma×fibroblast cell hybrids with those of parental cells, we have identified over 300 liver-enriched genes that are repressed at least 5-fold in the cell hybrids, the majority of which are repressed at least 10-fold. Also, we identify nearly 200 fibroblast-enriched genes that are repressed at least 5-fold. Silenced hepatic genes include several that encode transcription factors and proteins involved in signal transduction pathways. These data suggest that extensive reprogramming occurs in cell hybrids, leading to a nearly global (although not complete) loss of tissue-specific gene expression.

journal_name

Genomics

journal_title

Genomics

authors

Bulla GA,Luong Q,Shrestha S,Reeb S,Hickman S

doi

10.1016/j.ygeno.2010.08.006

subject

Has Abstract

pub_date

2010-12-01 00:00:00

pages

323-32

issue

6

eissn

0888-7543

issn

1089-8646

pii

S0888-7543(10)00181-3

journal_volume

96

pub_type

杂志文章

相关文献

GENOMICS文献大全
  • Revealing new landscape of cardiovascular disease through circular RNA-miRNA-mRNA axis.

    abstract::Non-coding RNA (ncRNA) is a kind of RNA, produced by genomic transcription and does not encode protein, but can regulate the function of genes, thus widely regulating pathological and physiological processes. The dynamic balance of the reticular structure between them is needed to regulate the homeostasis, the abnorma...

    journal_title:Genomics

    pub_type: 杂志文章,评审

    doi:10.1016/j.ygeno.2019.10.006

    authors: Su Q,Lv X

    更新日期:2020-03-01 00:00:00

  • Characterization of the polycystic kidney disease 2 gene promoter.

    abstract::The key regulatory elements for PKD2 transcription remain unclear. To identify these core elements, we characterized porcine PKD2 promoter with bioinformatics and molecular tools and found porcine PKD2 promoter bearing typical features of enriched CpG and less TATA. Further studies demonstrated that the core region wa...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2014.08.006

    authors: Wang Q,Han G,Ye J,Gao X,Niu H,Zhao J,Chai Y,Li N,Yin H

    更新日期:2014-12-01 00:00:00

  • Functional analysis of the murine Emr1 promoter identifies a novel purine-rich regulatory motif required for high-level gene expression in macrophages.

    abstract::This study has investigated the transcriptional regulation of the Emr1 gene in murine macrophages and defined an enhancer element within the proximal promoter that is necessary for Emr1 expression in myeloid cells. This element consists of an extended purine-rich sequence (PuRS) of 83 consecutive purine residues conta...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2004.08.016

    authors: O'Reilly D,Addley M,Quinn C,MacFarlane AJ,Gordon S,McKnight AJ,Greaves DR

    更新日期:2004-12-01 00:00:00

  • Statistical power for identifying nucleotide markers associated with quantitative traits in genome-wide association analysis using a mixed model.

    abstract::Use of mixed models is in the spotlight as an emerging method for genome-wide association studies (GWASs). This study investigated the statistical power for identifying nucleotide variants associated with quantitative traits using the mixed model methodology. Quantitative traits were simulated through design of herita...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2014.11.001

    authors: Shin J,Lee C

    更新日期:2015-01-01 00:00:00

  • DXS165 detects a translocation breakpoint in a woman with choroideremia and a de novo X; 13 translocation.

    abstract::The search for the gene for choroideremia (MIM 30310), a rare retinal dystrophy, has been of great interest due to the existence of several choroideremia patients with well-defined structural chromosome aberrations, thus providing the basis for a reverse genetics approach to the isolation of this disease gene. This re...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(90)90494-f

    authors: Merry DE,Lesko JG,Siu V,Flintoff WF,Collins F,Lewis RA,Nussbaum RL

    更新日期:1990-04-01 00:00:00

  • The gene for the serpin thrombin inhibitor (PI7), protease nexin I, is located on human chromosome 2q33-q35 and on syntenic regions in the mouse and sheep genomes.

    abstract::Protease nexin I (PNI) is the most important physiologic regulator of alpha-thrombin in tissues. PNI is highly expressed and developmentally regulated in the nervous system where it is concentrated at neuromuscular junctions and also central synapses in the hippocampus and striatum. Approximately 10% of identified pro...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.1025

    authors: Carter RE,Cerosaletti KM,Burkin DJ,Fournier RE,Jones C,Greenberg BD,Citron BA,Festoff BW

    更新日期:1995-05-01 00:00:00

  • The gene for the human putative apoE receptor is on chromosome 12 in the segment q13-14.

    abstract::We have previously described the cDNA coding for a new lipoprotein receptor that contains domains closely related to the ligand-binding domain of the LDL receptor. We have now investigated the localization of the gene for this new receptor by hybridization of the cDNA to panels of rodent cells containing subsets of hu...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(89)90087-6

    authors: Myklebost O,Arheden K,Rogne S,Geurts van Kessel A,Mandahl N,Herz J,Stanley K,Heim S,Mitelman F

    更新日期:1989-07-01 00:00:00

  • Physiological analysis and transcriptome sequencing reveal the effects of drier air humidity stress on Pterocarya stenoptera.

    abstract::Identifying physiological and transcriptomic changes can provide insights into the effects of drier air humidity stress on plants. In this study, we selected 6-month-old seedlings of Pterocarya stenoptera as study materials and used physiological index detection and transcriptome sequencing to investigate the adaptati...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2020.09.027

    authors: Ye XF,Li Y,Liu HL,He YX

    更新日期:2020-11-01 00:00:00

  • Cloning, sequencing, gene organization, and localization of the human ribosomal protein RPL23A gene.

    abstract::The intron-containing gene for human ribosomal protein RPL23A has been cloned, sequenced, and localized. The gene is approximately 4.0 kb in length and contains five exons and four introns. All splice sites exactly match the AG/GT consensus rule. The transcript is about 0.6 kb and is detected in all tissues examined. ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.5038

    authors: Fan W,Christensen M,Eichler E,Zhang X,Lennon G

    更新日期:1997-12-01 00:00:00

  • Effect of selenocystine on gene expression profiles in human keloid fibroblasts.

    abstract::In this study, selenocystine, a nutritionally available selenoamino acid, was identified for the first time as a novel agent with anti proliferative activity on human keloids. The 20 μM concentration after 48 h treatment used here was the most effective to reduce keloid fibroblast growth. We analyzed the gene expressi...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2011.02.009

    authors: De Felice B,Garbi C,Wilson RR,Santoriello M,Nacca M

    更新日期:2011-05-01 00:00:00

  • Bisulfite genomic sequencing-derived methylation profile of the xist gene throughout early mouse development.

    abstract::Differential epigenetic modification by methylation of CpG dinucleotides is a candidate mechanism that may identify the alleles of imprinted genes and result in monoallelic expression of either the maternal or the paternal allele. Determination of the allelic methylation status of imprinted genes in the gametes and du...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5570

    authors: McDonald LE,Paterson CA,Kay GF

    更新日期:1998-12-15 00:00:00

  • Cloning and chromosome localization of the mouse Ews gene.

    abstract::The human EWS gene encodes a putative RNA binding protein. As a result of acquired chromosome rearrangement, the N-terminal portion of the EWS protein is fused to the DNA binding domain of either FLI-1 or ERG in the Ewing family of tumors and to the DNA binding domain of ATF1 in malignant melanoma of soft parts. We ha...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1495

    authors: Plougastel B,Mattei MG,Thomas G,Delattre O

    更新日期:1994-09-01 00:00:00

  • A genetic linkage map of 17 markers on human chromosome 21.

    abstract::We have constructed a genetic linkage map of 17 markers on the long arm of human chromosome 21, including six genes and two anonymous loci with a variable number of tandem repeats. The estimated length of the map is 103 cM in males and 140 cM in females, assuming Kosambi interference. Recombination in females was appr...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(89)90282-6

    authors: Warren AC,Slaugenhaupt SA,Lewis JG,Chakravarti A,Antonarakis SE

    更新日期:1989-05-01 00:00:00

  • Regional localization of human chromosome 15 loci.

    abstract::One hundred forty-nine chromosome 15 loci were mapped by PCR with respect to chromosome breakpoints in three somatic cell hybrids retaining total or part of chromosome 15 and to a 10-Mb YAC contig. This chromosome was subdivided into 5 regions, yielding an average resolution of more than 1 sequence tagged site per meg...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1550

    authors: Richard I,Broux O,Chiannilkulchai N,Fougerousse F,Allamand V,Bourg N,Brenguier L,Devaud C,Pasturaud P,Roudaut C

    更新日期:1994-10-01 00:00:00

  • Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

    abstract::Ultraconservation has been variously defined to describe sequences that have remained identical or nearly so over long periods of evolution to a degree that is higher than expected for sequences under typical constraints associated with protein-coding sequences, splice sites, or transcription factor binding sites. Mos...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2009.07.005

    authors: Rödelsperger C,Köhler S,Schulz MH,Manke T,Bauer S,Robinson PN

    更新日期:2009-11-01 00:00:00

  • VennBLAST—whole transcriptome comparison and visualization tool.

    abstract::RNA-seq is the method of choice for getting a primary list of genes for non-model organisms. Once this is achieved, one would proceed to annotate the newly discovered genes and consequently strive to position the organism in an evolutionary context. These kinds of studies involving high-throughput sequencing generate ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2014.12.004

    authors: Zahavi T,Stelzer G,Strauss L,Salmon AY,Salmon-Divon M

    更新日期:2015-03-01 00:00:00

  • Transcriptome profiling and dimorphic expression of sex-related genes in fifth-instar nymphs of Sogatella furcifera, an important rice pest.

    abstract::Sogatella furcifera is an important rice pest. In order to understand the molecular basis of the sex determination in this pest, we performed de novo transcriptome sequencing of six cDNA libraries (three biological replicates) of female and male fifth-instar nymphs. Total 65,199 unigenes were obtained, with an average...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2019.06.024

    authors: Lin J,He J,Liang A,Wang F

    更新日期:2020-03-01 00:00:00

  • Cloning and chromosomal mapping of three novel genes, GPR9, GPR10, and GPR14, encoding receptors related to interleukin 8, neuropeptide Y, and somatostatin receptors.

    abstract::We employed the polymerase chain reaction and genomic DNA library screening to clone novel human genes, GPR9 and GPR10, and a rat gene, GPR14. GPR9, GPR10, and GPR14 each encode G protein-coupled receptors. GPR10 and GPR14 are intronless within their coding regions, while GPR9 contains at least one intron. The recepto...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.9996

    authors: Marchese A,Heiber M,Nguyen T,Heng HH,Saldivia VR,Cheng R,Murphy PM,Tsui LC,Shi X,Gregor P

    更新日期:1995-09-20 00:00:00

  • Linkage mapping of human chromosome 10 microsatellite polymorphisms.

    abstract::Ten microsatellite DNA polymorphisms located on human chromosome 10 were regionally mapped using subchromosomal somatic cell hybrids and linkage analysis. The resulting order of the markers from pter-qter was [D10S89, D10S111], D10S107, D10S109, [D10S91, D10S110, D10S108, D10S88, D10S168], and D10S169. Order of the ma...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(92)90455-2

    authors: Decker RA,Moore J,Ponder B,Weber JL

    更新日期:1992-03-01 00:00:00

  • Localization of the zinc finger DNA-binding protein HIV-EP1/MBP-1/PRDII-BF1 to human chromosome 6p22.3-p24.

    abstract::A variety of cellular proteins have been found to bind to related DNA sequences in the enhancer elements of the human immunodeficiency virus, the kappa immunoglobulin gene, the class I major histocompatibility complex gene, and the beta-interferon gene. Recently, lambda gt11 gene expression cloning using ligated oligo...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90371-k

    authors: Gaynor RB,Muchardt C,Diep A,Mohandas TK,Sparkes RS,Lusis AJ

    更新日期:1991-04-01 00:00:00

  • The alpha-fetoprotein promoter is the target of Afr1-mediated postnatal repression.

    abstract::The alpha-fetoprotein (AFP) gene is transcribed at high levels in the fetal liver and is repressed at birth, leading to low but detectable levels of AFP mRNA in the adult liver. This repression is regulated, in part, by a locus that is unlinked to AFP called Alpha-fetoprotein regulator 1 (Afr1). Previous studies showe...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.6073

    authors: Peyton DK,Huang MC,Giglia MA,Hughes NK,Spear BT

    更新日期:2000-01-15 00:00:00

  • Physical mapping studies on the human X chromosome in the region Xq27-Xqter.

    abstract::We have characterized three terminal deletions of the long arm of the X chromosome. Southern analysis using Xq27/q28 probes suggests that two of the deletions have breakpoints near the fragile site at Xq27.3. Flow karyotype analysis provides an estimate of 12 X 10(6) bp for the size of the deleted region. We have not ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(87)90028-0

    authors: Patterson M,Schwartz C,Bell M,Sauer S,Hofker M,Trask B,van den Engh G,Davies KE

    更新日期:1987-12-01 00:00:00

  • Large-scale physical mapping within the region 22q12.3-13.1 in meningioma.

    abstract::The lack of physical mapping data strongly restricts the analysis of the meningioma chromosomal region that was assigned to the bands 22q12.3-qter. Recently, we reported a new marker D22S16 for chromosome 22 that was assigned to the region 22q13-qter by in situ hybridization. Utilizing somatic cell hybrids we now subl...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90196-l

    authors: Herzog R,Gottert E,Henn W,Zang K,Blin N,Trent J,Meese E

    更新日期:1991-08-01 00:00:00

  • Construction of a 1.2-Mb contig surrounding, and molecular analysis of, the human CREB-binding protein (CBP/CREBBP) gene on chromosome 16p13.3.

    abstract::In the interest of cloning and analyzing the genes responsible for two very different diseases, the Rubinstein-Taybi syndrome (RTS) and acute myeloid leukemia (AML) associated with the somatic translocation t(8;16)(p11;p13.3), we constructed a high-resolution restriction map of contiguous cosmids (contig) covering 1.2...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4699

    authors: Giles RH,Petrij F,Dauwerse HG,den Hollander AI,Lushnikova T,van Ommen GJ,Goodman RH,Deaven LL,Doggett NA,Peters DJ,Breuning MH

    更新日期:1997-05-15 00:00:00

  • A high-resolution genetic map of the nervous locus on mouse chromosome 8.

    abstract::The nervous (nr) mutant mouse displays two gross recessive traits: both an exaggeration of juvenile hyperactivity and a pronounced ataxia become apparent during the third and fourth postnatal weeks. Using an intersubspecific intercross, we have established a high-resolution map of a segment of mouse chromosome 8 that ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.5193

    authors: De Jager PL,Harvey D,Polydorides AD,Zuo J,Heintz N

    更新日期:1998-03-15 00:00:00

  • Whole-genome methylation profiling from PBMCs in acute-exacerbation COPD patients with good and poor responses to corticosteroid treatment.

    abstract::Identifying heterogeneity in chronic obstructive pulmonary disease (COPD) phenotypes is important for the development of personalized medicine. Genome-wide analysis was used to compare the methylation levels of peripheral blood mononuclear cell (PBMC) samples from 24 acute-exacerbation (AE) COPD patients with good/poo...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2018.09.010

    authors: Lee SW,Hwang HH,Hsu PW,Chuang TY,Liu CW,Wu LS

    更新日期:2019-12-01 00:00:00

  • Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution.

    abstract::Fluorescence in situ hybridization mapping of fully integrated human BAC clones to primate chromosomes, combined with precise breakpoint localization by PCR analysis of flow-sorted chromosomes, was used to analyze the evolutionary rearrangements of the human 3q21.3-syntenic region in orangutan, siamang gibbon, and sil...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2004.10.007

    authors: Yue Y,Grossmann B,Ferguson-Smith M,Yang F,Haaf T

    更新日期:2005-01-01 00:00:00

  • PCR amplification of chromosome-specific DNA isolated from flow cytometry-sorted chromosomes.

    abstract::We have established a method for amplifying and obtaining large quantities of chromosome-specific DNA by linker/adaptor ligation and polymerase chain reaction (PCR). Small quantities of DNA isolated from flow cytometry-sorted chromosomes 17 and 21 were digested with MboI, ligated to a linker/adaptor, and then subjecte...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(92)90378-6

    authors: Chang KS,Vyas RC,Deaven LL,Trujillo JM,Stass SA,Hittelman WN

    更新日期:1992-02-01 00:00:00

  • A dicistronic gene pair within a cluster of "EF-hand" protein genes in the genomes of Drosophila species.

    abstract::Androcam is a Drosophila melanogaster calmodulin-related protein that functions specifically in the testis. We show that the Acam gene is part of a cluster of three intronless genes arranged in a head-to-tail manner. The additional genes also encode calmodulin-related proteins with testis-specific transcription. Acam ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2006.04.009

    authors: Pavlik P,Konduri V,Massa E,Simonette R,Beckingham KM

    更新日期:2006-09-01 00:00:00

  • Rapid isolation of DNA probes within specific chromosome regions by interspersed repetitive sequence polymerase chain reaction.

    abstract::A method was recently developed for the specific amplification of human DNA sequences from interspecific somatic cell hybrids by the polymerase chain reaction (PCR) using primers directed to Alu, a short interspersed repeat element (SINE). We now show human-specific amplification using a primer to the 3' end of the hu...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(90)90477-c

    authors: Ledbetter SA,Nelson DL,Warren ST,Ledbetter DH

    更新日期:1990-03-01 00:00:00